Before adding any more parameter updaters, we need to get organized with respect to the output generated by our program. Most Bayesian phylogenetic MCMC software stores sampled tree topologies and edge lengths in a tree file, sampled model parameter values in a parameter file, and sends other output to the console.
This step of the tutorial is devoted to creating an OutputManager class that will handle all these things. It will open a tree file and a parameter file before MCMC sampling begins, save sampled trees and parameters to their respective files during the run, and close these files when sampling is finished. Also, we will send messages to the OutputManager and the OutputManager will take care of displaying these to the console.
| Step | Title | Description |
| Step 15.1 | The OutputManager Class | Create the OutputManager class |
| Step 15.2 | Adding Helper Functions to Data and Model | Integrate the OutputManager class into the Data and Model classes |
| Step 15.3 | Modify Strom | Integrate the OutputManager class into the Strom class. |
| Step 15.4 | Test the OutputManager class | . |